Antibiotics and antibacterials are present in water bodies worldwide but little is known about their effects on the biological processes often used to treat water. In this research, the effect of antibiotics on bacterial activity and community structure was investigated by growing biofilms in the presence and absence of a mixture of three compounds (sulfamethoxazole, erythromycin, and ciprofloxacin) in a continuous-flow rotating annular bioreactor fed acetate as a carbon and energy source. Steady-state, surface area-normalized substrate utilization rates for all antibiotic treatments (all at 0.33μgL-1, all at 3.33μgL-1, and 1 at 3.33μgL-1 with the other 2 at 0.33μgL-1) were similar to the control experiments. Higher attached biomass levels in the experiments with ciprofloxacin at 3.33μgL-1 resulted in lower steady-state biomass-normalized substrate utilization rates in comparison to other runs. Microbial community analyses via automated ribosomal intergenic spacer analysis revealed significant shifts in community structure for the experiments dosed with the highest concentrations of ciprofloxacin, suggesting that the antibiotic selected for more resistant bacterial strains. The results of this research also suggest that mixtures of antibiotics at the sub-μgL-1 concentrations typically observed in surface waters are unlikely to affect biological process performance, at least in terms of the degradation of easily assimilable compounds. Conversely, changes to community structure and biofilm quantity might be expected with ciprofloxacin at μgL-1 concentrations.